Package: beadplexr 0.5.0.999

beadplexr: Analysis of Multiplex Cytometric Bead Assays

Reproducible and automated analysis of multiplex bead assays such as CBA (Morgan et al. 2004; <doi:10.1016/j.clim.2003.11.017>), LEGENDplex (Yu et al. 2015; <doi:10.1084/jem.20142318>), and MACSPlex (Miltenyi Biotec 2014; Application note: Data acquisition and analysis without the MACSQuant analyzer; <https://www.miltenyibiotec.com/upload/assets/IM0021608.PDF>). The package provides functions for streamlined reading of fcs files, and identification of bead clusters and analyte expression. The package eases the calculation of standard curves and the subsequent calculation of the analyte concentration.

Authors:Ulrik Stervbo [aut, cre]

beadplexr_0.5.0.999.tar.gz
beadplexr_0.5.0.999.zip(r-4.7)beadplexr_0.5.0.999.zip(r-4.6)beadplexr_0.5.0.999.zip(r-4.5)
beadplexr_0.5.0.999.tgz(r-4.6-any)beadplexr_0.5.0.999.tgz(r-4.5-any)
beadplexr_0.5.0.999.tar.gz(r-4.7-any)beadplexr_0.5.0.999.tar.gz(r-4.6-any)
beadplexr_0.5.0.999.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
beadplexr/json (API)

# Install 'beadplexr' in R:
install.packages('beadplexr', repos = c('https://ustervbo.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://gitlab.com/ustervbo/beadplexr

Datasets:
  • lplex - LEGENDplex example data
  • simplex - Simulated beadplex data

On CRAN:

Conda:

5.10 score 42 scripts 325 downloads 2 mentions 31 exports 89 dependencies

Last updated from:887b760902. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK189
source / vignettesOK616
linux-release-x86_64OK223
macos-release-arm64OK189
macos-oldrel-arm64OK195
windows-develOK143
windows-releaseOK137
windows-oldrelOK148
wasm-releaseOK128

Exports:approx_adjustas_data_frame_analytebp_clarabp_dbscanbp_density_cutbp_kmeansbp_mclustcalc_analyte_mficalc_std_conccalculate_concentrationdensity_cutdespeckledist_chebyshevdo_find_turning_pointsfacs_density1dfacs_density2dfacs_hexbinfacs_plotfacs_scatterfit_standard_curveidentify_analyteidentify_cba_analyteidentify_legendplex_analyteidentify_macsplex_analyteload_panelplot_estimateplot_std_curveplot_target_est_concread_fcstrim_populationturning_point

Dependencies:abindbackportsbootbroomcarcarDataclasscliclustercodetoolscolorspacecowplotcpp11DEoptimRDerivdiptestdoBydplyrdrcfarverflexmixforecastFormulafpcfracdiffgenericsggplot2gluegtablegtoolsisobandkernlablabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmclustmgcvmicrobenchmarkminqamodelrmodeltoolsmultcompmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigplotrixprabcluspurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrobustbaseS7sandwichscalesSparseMstringistringrsurvivalTH.datatibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithryamlzoo

Analysis of LEGENDplex data with beadplexr
Introduction | Naming LEGENDplex data-files | Reading FACS data | Load panel information | Get analyte MFI | Finding the analysis settings | Bead groups A and B | Bead IDs | Putting it all together | Calculate analyte concentration | Fit the standard curve | Estimate sample analyte concentration | Session info
Rendered fromlegendplex_analysis.Rmdusingknitr::rmarkdown

Last update: 2023-06-13
Started: 2020-04-04

beadplexr with CBA and MACSPlex assays
Introduction | Load and view the data | The MACSPlex-like data | The CBA-like data | Analyte identification | MACSPlex-like | CBA-like | ID assignment | Noise reduction | Session info
Rendered fromcba_macsplex_example.Rmdusingknitr::rmarkdown

Last update: 2023-06-13
Started: 2018-03-06

Preparing flow-data for use with with beadplexr
Introduction | Reading FACS data | Applying the event filter | Pseudo-color plots | Copy-paste code
Rendered frompreparing_flow_data.Rmdusingknitr::rmarkdown

Last update: 2023-06-13
Started: 2020-04-04

Readme and manuals

Help Manual

Help pageTopics
Approximate bandwidth adjustment.approx_adjust
Cast list of analytes to 'data.frame'as_data_frame_analyte
Calculate the analyte intensitycalc_analyte_mfi
Calculate standard concentrationcalc_std_conc
Calculate concentration.calculate_concentration
Clustering with trimmingbp_clara bp_dbscan bp_density_cut bp_kmeans bp_mclust cluster_events
Despeckle parametersdespeckle
Chebyshev distancedist_chebyshev
Plot FACS data.facs_density1d facs_density2d facs_hexbin facs_plot facs_scatter
Fit a standard curvefit_standard_curve
Identify analyteidentify_analyte
Identify multiplex assay analytesidentify_assay_analyte identify_cba_analyte identify_legendplex_analyte identify_macsplex_analyte
Load panel informationload_panel
LEGENDplex example datalplex
Plot concentrationsplot_concentrations plot_estimate plot_std_curve plot_target_est_conc
Read a fcs file.read_fcs
Simulated beadplex datasimplex
Trim cluster.trim_population
Turning pointsturning_point